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At least 163 records · Page 9Linked to original sources
PubMed2003

[The association of paraoxonase 2 gene C311S variant with ischemic stroke in Chinese type 2 diabetes mellitus patients].

OBJECTIVE: To investigate the association between the C311S polymorphism of paraoxonase 2 (PON2) gene and ischemic stroke in Chinese type 2 diabetes mellitus (T2DM) patients. METHODS: A case-control study of 279 Chinese subjects (including 162 T2DM with or without ischemic stroke and 117 non-diabetic control) was performed. Genotype frequencies of C311S polymorphism were studied by polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) analysis with DdeI digestion. RESULTS: C311S polymorphism of PON2 gene was detected in Chinese with the C/S allele frequencies 0.145 and 0.855. The frequency distribution showed significant difference between Chinese and Asian Indian. Furthermore, the genotype distribution (SS, CS and CC) of the PON2 C311S gene polymorphism exhibited a significant difference between T2DM patients complicated with ischemic stroke and T2DM without ischemic stroke, the former had a significantly higher C allele frequency(P<0.05). CONCLUSION: The above data indicate that the polymorphism at codon 311(Cys --> Ser)in the PON2 gene is associated with ischemic morbidity in Chinese T2DM patients and C allele might be a risk factor.

Adult↗
PubMed2004

P53 codon 72 polymorphism and risk of gastric cancer in a Chinese population.

The p53 gene plays an important role in cell cycle control in response to DNA damage, which may increase the probability of mutations that lead to carcinogenesis. The p53 codon 72 Arg right curved arrow Pro polymorphism has been suggested to be associated with risk for different kind of cancers, but the data on gastric cancer (GC) is very limited. To evaluate the association between this polymorphism and risk of GC, we performed genotype analysis by using a polymerase chain reaction-based restriction fragment length polymorphism assay in a population-based case-control study of 324 GC patients and 317 cancer-free controls in a Chinese population. The controls were frequency-matched to the cases by age, sex and smoking status. The frequency of the p53 Arg allele was 57.4% in the cases and 54.9% in the controls, and the genotype frequencies of p53 Arg/Arg, Arg/Pro, and Pro/Pro were 29.6%, 55.6%, and 14.8%, respectively, in the cases, and 29.6%, 50.5%, and 19.9%, respectively, in the controls (p=0.207). Logistic regression analysis revealed that the p53 Arg allele (Arg/Pro and Arg/Arg genotype) was associated with a borderline significantly increased risk of gastric cancer (adjusted OR=1.44, 95% CI=0.95-2.18), particularly non-cardia gastric cancer (adjusted OR=1.67, 95% CI=1.00-2.77), compared with p53 homozygous Pro allele (Pro/Pro genotype), and the risk was significantly more evident among alcohol drinkers (adjusted OR=2.85, 95% CI=1.37-5.95). While the results suggest that the p53 codon 72 polymorphism may contribute to gastric cancer susceptibility, further larger studies are needed to substantiate our findings and to explore a possible interaction between p53 codon 72 polymorphism and alcohol in the etiology of gastric cancer.

Adult↗
PubMedDate not supplied

Implementation of garlic cryopreservation techniques in the national plant germplasm system.

The USDA-ARS National Plant Germplasm System (NPGS) maintains more than 200 Allium sativum (garlic) accessions at the Western Regional Plant Introduction Station in Pullman, WA. All accessions must be grown out in the field annually since garlic plants from these accessions do not reliably produce seeds and bulbs do not store well. Shoot tips excised from garlic cloves can be successfully cryopreserved using either Plant Vitrification Solution 2 (PVS2; 15 percent v/v DMSO, 15 percent v/v ethylene glycol, 30 percent v/w glycerol, 0.4 M sucrose) or Plant Vitrification Solution 3 (PVS3; 50 percent v/w sucrose, 50 percent v/w glycerol). We compared regrowth of shoot tips representing diverse garlic germplasm after exposure to either PVS2 or PVS3 during the cryopreservation procedure. At the USDA-ARS National Center for Genetic Resources Preservation, a component of the NPGS, we consider accessions successfully preserved if a minimum of 40 percent of explants exhibit regrowth after liquid nitrogen exposure and at least 60 viable shoot tips remain in long-term storage. Ten of twelve diverse garlic accessions were successfully cryopreserved using either PVS2 or PVS3 as cryoprotectants. Five genotypes had the best post liquid nitrogen regrowth after exposure to PVS2, four genotypes had the best regrowth after exposure to PVS3, and three genotypes performed equally well using either cryoprotectant solution. This project is part of an ongoing program to cryopreserve accessions of NPGS clonal crop collections.

Cryopreservation↗
PubMed1996

Genetic evidence for the Lewis enzyme, which synthesizes type-1 Lewis antigens in colon tissue, and intracellular localization of the enzyme.

To determine whether the Lewis enzyme responsible for the Lewis blood type antigens on erythrocytes synthesizes the Lewis antigens on normal cells and cancer cells in colon tissue, we performed genotyping of the Lewis gene by the PCR-RFLP method and by immunohistochemical staining of Lewis antigens and the Lewis enzyme with specific monoclonal antibodies (mAbs) in colon tissues obtained from 100 colon cancer patients. Five of the 100 patients were identified as homozygotes for the mutant Lewis gene, i.e., the le/le genotype that cannot encode functional Lewis enzyme. The cells in both the normal and cancerous regions of colon tissue from these five le/le patients were completely devoid of staining with mAbs against Lewis antigens with the type 1 chain, i.e., Lewis a, Lewis b, and sialyl Lewis a. In contrast, the cells in cancerous regions of the colon tissue of the 95 patients with the Le/Le or Le/le genotype positively stained with all three mAbs, anti-Lewis a, anti-Lewis b, and anti-sialyl Lewis a. The cells in the cancerous regions of the colon tissue of the five le/le patients stained with DU-PAN-2 mAb, whose recognizing epitope is known to be sialyl Lewis c, a precursor structure of sialyl Lewis a. By immunohistochemical staining with FTA 1-16 mAb, which is directed at the human Lewis enzyme, we were able to demonstrate for the first time that the enzyme is localized in the Golgi area of the colon epithelial cells of patients with the Le/Le or Le/le genotype. No staining was observed in the Golgi area of the cells of the patients with the le/le genotype. From these results, we conclude that individuals with the Le/Le or Le/le genotype possess a functional Lewis enzyme synthesizing fucosylated type-1 Lewis antigens in the Golgi apparatus of the colon epithelial cells, but that individuals with the le/le genotype are devoid of the Lewis enzyme in the Golgi apparatus, resulting in an inability to synthesize Lewis antigens with the type-1 chain, and that it is inappropriate to use CA19-9, whose antigenic epitope is defined as sialyl Lewis a, as a tumor marker in patients with the le/le genotype.

Antibodies, Monoclonal↗
PubMed1998

Exfoliated ductal epithelial cells in human breast milk: a source of target tissue DNA for molecular epidemiologic studies of breast cancer.

Studies of biomarkers of putative breast carcinogens, such as DNA adducts, have been limited by the difficulty in obtaining representative ductal epithelial cells (DECs) from breast tissue. In this feasibility study, we sought to ascertain if exfoliated DECs in breast milk could be a source of DNA for biomarker studies. Specimens (n = 38) were collected over 24 h from nursing women, and a questionnaire was administered. Cell pellets were isolated by repeated centrifugation and washing. Pellets were resuspended and incubated for 2 h, with glass adherence used to remove monocytes, resulting in an enrichment of DECs of >80%. Nonadherent cells were removed, washed, and homogenized for DNA isolation. Accurate DNA quantification was performed by 32P-postlabeling of normal nucleotides under conditions of excess ATP. Although there was wide variability in the amounts of DNA recovered, DNA yield was significantly associated with the number of weeks postpartum (P < 0.01), with optimal yield between 6 and 8 weeks after birth. There were no significant associations (P < 0.05) between the number of cells recovered and milk volume, method of collection, or the number of samples in a 24-h period per individual. This study demonstrates that breast milk can be used as a source of DECs for biomarker studies of gene-environment interaction and that sufficient DNA can be recovered to evaluate carcinogen-DNA adducts and to perform genotyping assays. Using this approach, exfoliated DECs may serve as a source of representative cells for studies of breast carcinogenesis and biomarkers of exposure, susceptibility, and effect.

Biomarkers, Tumor↗
PubMed1998

[Occurrences of penicillin-binding protein 2B gene in clinically isolated penicillin-resistant Streptococcus pneumoniae].

We analyzed 88 strains of Streptococcus pneumoniae (S. pneumoniae) isolated in Showa University Hospital from June 1995 to July 1996. The ratios of antibiotic resistance were 39% to penicillin G, 50% to erythromycin, and 2% to imipenem. No resistant to cefotaxime and ofloxacin was observed. Thirty-four strains (39%) were considered to be penicillin-resistant S. pneumoniae (PRSP) strains (MIC of penicillin G > or = 0.5 microgram/ml), according to the breakpoint determined by the Japanese Working Group for Penicillin-Resistant Streptococcus pneumoniae. The ratio of PRSP was higher in S. pneumoniae isolated from inpatients (25/47) when compared to that from outpatients. By PCR analysis, DNA regions of autolysin were amplified in all the 88 strains, confirming that the isolates were S. pneumoniae. Penicillin-binding protein 2B (PBP2B) class B region was positive in 32 strains, and PBP2B class A was in 2 strains. Twenty eight of 34 strains of PRSP contained the PBP2B class B gene. In the remaining six PRSP strains, neither the PBP2B class A nor B region was amplified. The PBP2B class B region was detected as a 180-kb fragment of SmaI digestion of S. pneumoniae DNA by Southern blot analysis, confirming that the detection of PBP2B class B gene by PCR is reliable. We concluded that the PBP2B class B gene is considered to be a major gene responsible for phenotypic resistance of PRSP. We performed genotyping by SmaI digestion pattern using pulsed field gel electrophoresis. No identical pattern was observed in isolates from inpatients, suggesting that apparent nosocomial infection of S. pneumoniae was negligible.

Aminoacyltransferases↗
PubMed2002

[Relationship of growth hormone (GH 2) genotypes with some production performances in pig].

The genotypes of 117 Nanchang White pigs and 361 Large Yorkshire pigs at GH 2 locus were detected by PCR-RFLP. The PCR products were cut by Apa I, and produced two alleles: A(449 + 101 + 55 bp), and B(316 + 133 + 101 + 49 bp). Effects of different genotypes on some important production traits involving the birth weight, 2-month body weight, 6-month body weight, corrected back-fat thickness, average back-fat thickness, feed to gain ratio and lean percentage were analyzed. The results showed that in Nanchang White pigs, no significant differences were observed between different genotypes and different growth and carcass traits; while in Large Yorkshire, the pigs with BB genotype had more lean percentage than pigs with AA genotype (P < 0.05).

Adipose Tissue↗
PubMed2006

Performance of the genotype MTBDR line probe assay for detection of resistance to rifampin and isoniazid in strains of Mycobacterium tuberculosis with low- and high-level resistance.

We assessed the performance of the Genotype MTBDR line probe assay that offers the simultaneous identification of Mycobacterium tuberculosis and its resistance to rifampin (RIF) and isoniazid (INH) by detecting the most commonly found mutations in the rpoB and katG genes. One hundred thirteen M. tuberculosis isolates were tested. The nucleotide sequences of the katG and inhA genes and the mabA-inhA promoter region were also determined. The MTBDR assay detected 100% and 67% (n = 64) of the strains resistant to RIF and INH, respectively. Among the latter, 62 strains carried a Ser315Thr mutation in katG, 59 of them displaying a high level of resistance to INH. Two strains with a low level of INH resistance had a Ser315Asn mutation. No mutation was found by the MTBDR assay for 31 INH-resistant strains (33%), of which 24 showed a low level of resistance. By DNA sequencing, we found among them various mutations in the KatG protein for 7 strains, a C-->T mutation in position -15 of the mabA-inhA promoter in 17 strains, and a Ser94Ala mutation in InhA for 7 strains. In conclusion, the MTBDR assay, which fits easily in the workflow of a routine laboratory, enabled the detection of 100% of the RIF-resistant strains and 89% of the INH-resistant strains with a high level of resistance but only 17% of the strains characterized by a low level of INH resistance, indicating that the test can be used as a rapid method to detect in the same experiment the rifampin-resistant and the high-level isoniazid-resistant strains of M. tuberculosis.

Antitubercular Agents↗
PubMed2003

APOE genotype, memory test performance, and the risk of Alzheimer's disease in the Canadian Study of Health and Aging.

OBJECTIVES: This study examined the relation between two risks for Alzheimer's disease (AD): the apolipoprotein (APOE) epsilon4 allele and poor memory test performance. METHODS: In the Canadian Study of Health and Aging (CSHA), a 5-year longitudinal population-based study that screened and followed over 10,000 participants, 2,914 had an initial clinical assessment and 1,624 had APOE genotype testing. All participants were categorized as having no cognitive impairment, cognitive impairment but no dementia, or dementia at both baseline and follow-up. We examined those (n = 209) with a complete neuropsychological assessment at baseline and no evidence of cognitive impairment who had either APOE epsilon3/epsilon3 or epsilon3/epsilon4 genotypes and who had a clinical consensus diagnosis of either no cognitive impairment or AD at follow-up. Delayed free recall memory was evaluated at CSHA-1 with the Buschke Cued Recall Test (BCRT). RESULTS: The risk of AD at follow-up was increased for participants with an APOE epsilon3/epsilon4 genotype when memory test performance was not considered, but logistic regression demonstrated that a model which also considered baseline memory test performance was more predictive of AD. In the more complete model, reduced BCRT free recall scores were associated with an increased risk of AD, whereas the risk associated with the APOE epsilon3/epsilon4 genotype was no longer significant. CONCLUSIONS: For those with no evidence of cognitive impairment, drawn from a population-based sample of elderly persons, the APOE epsilon3/epsilon4 genotype was only associated with an increased risk of AD after 5 years if their memory test performance was relatively poor at baseline. Regardless of the APOE genotype, and in the absence of clinical evidence of cognitive impairment, reduced scores on a test of delayed free recall at baseline was associated with an increased risk of AD after 5 years.

Aged↗
PubMed2007

Effect of genotype on slaughtering performance and meat physical and sensory characteristics of organic laying hens.

Slaughtering yields and some meat physical and sensorial parameters of laying hens reared under organic system production were studied. The hens belonged to both Italian dual-purpose breeds [Ermellinata di Rovigo (ER; brown eggshell) and Robusta Maculata (RM; brown eggshell)] as well as hybrid genotypes [Hy Line White 36 (white eggshell) and Hy Line Brown (brown eggshell)]. The birds were reared under organic farming system production from 24 to 44 wk of age, when they were slaughtered. They were reared throughout summer and autumn, and the temperature ranged from about 28 to 3 degrees C. Local breeds presented higher (P < 0.01) live BW and dressing percentage compared with hybrids. The RM and ER carcasses had (P < 0.01) the highest breast and leg (thigh and drumstick) percentage, respectively. The muscle-bone ratio of the Hy Line White 36 drumstick was lower (P < 0.05) than the RM ratio, whereas the other groups were intermediate. The ER breast presented the highest (P < 0.01) lightness value and the lowest (P < 0.01) final pH value compared with the other 3 groups. The breast meat significantly differed according to genotype for almost all the studied sensorial parameters (adhesivity, fibrousness, chewiness, solubility, juiciness, tenderness, shear resistance), with the exception of aroma and odor intensity. In the thigh, genotype significantly affected aroma, adhesivity, fibrousness, solubility, tenderness, and shear resistance.

Abattoirs↗
PubMed1996

Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA.

Genetic analysis of limiting quantities of genomic DNA play an important role in DNA forensics, paleoarcheology, genetic disease diagnosis, genetic linkage analysis, and genetic diversity studies. We have tested the ability of degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) to amplify picogram quantities of human genomic DNA for the purpose of increasing the amount of template for genotyping with microsatellite repeat markers. DNA was uniformly amplified at a large number of typable loci throughout the human genome with starting template DNAs from as little as 15 pg to as much as 400 ng. A much greater-fold enrichment was seen for the smaller genomic DOP-PCRs. All markers tested were amplified from starting genomic DNAs in the range of 0.6-40 ng with amplifications of 200- to 600-fold. The DOP-PCR-amplified genomic DNA was an excellent and reliable template for genotyping with microsatellites, which give distinct bands with no increase in stutter artifact on di-, tri-, and tetranucleotide repeats. There appears to be equal amplification of genomic DNA from 55 of 55 tested discrete microsatellites implying near complete coverage of the human genome. Thus, DOP-PCR appears to allow unbiased, hundreds-fold whole genome amplification of human genomic DNA for genotypic analysis.

DNA↗
PubMed2000

Improved version 2.0 qualitative and quantitative AMPLICOR reverse transcription-PCR tests for hepatitis C virus RNA: calibration to international units, enhanced genotype reactivity, and performance characteristics.

Version 2.0 qualitative and quantitative AMPLICOR reverse transcription-PCR tests for HCV were designed to improve on the performance of first version of the hepatitis C virus (HCV) tests. The new tests were calibrated in international units, the new commonly accepted standard unit of measurement for HCV RNA. The sensitivity of the qualitative tests was enhanced by modifying the specimen processing procedure to achieve a limit of detection 50 IU/ml. The limit of detection for the quantitative tests was 600 IU/ml. Modifications to the amplification reaction mixture and thermal cycling conditions enabled all genotypes to be amplified with similar efficiency. The quantitative tests exhibited a linear range extending from 500 to 500,000 IU/ml and excellent reproducibility, with coefficients of variation ranging from 18 to 39%, within the linear range. These data indicate that the version 2. 0 AMPLICOR HCV tests will improve diagnosis of HCV infection and will yield more-accurate titers for prognosis and for monitoring therapeutic efficacy, particularly at low viral loads. Furthermore, it will be possible to compare the performance characteristics and viral load measurements of AMPLICOR tests to those of other tests that adopt the international unit as the standard of measurement.

Calibration↗
PubMed2002

Evaluation of performance of four genotypic methods for studying the genetic epidemiology of Aspergillus fumigatus isolates.

In the present investigation, 49 Aspergillus fumigatus isolates obtained from four nosocomial outbreaks were typed by Afut1 restriction fragment length polymorphism (RFLP) analysis and three PCR-based molecular typing methods: random amplified polymorphic DNA (RAPD) analysis, sequence-specific DNA primer (SSDP) analysis, and polymorphic microsatellite markers (PMM) analysis. The typing methods were evaluated with respect to discriminatory power (D), reproducibility, typeability, ease of use, and ease of interpretation to determine their performance and utility for outbreak and surveillance investigations. Afut1 RFLP analysis detected 40 types. Thirty types were observed by RAPD analysis. PMM analysis detected 39 allelic types, but SSDP analysis detected only 14 types. All four methods demonstrated 100% typeability. PMM and RFLP analyses had comparable high degrees of discriminatory power (D = 0.989 and 0.988, respectively). The discriminatory power of RAPD analysis was slightly lower (D = 0.971), whereas SSDP analysis had the lowest discriminatory power (D = 0.889). Overall, SSDP analysis was the easiest method to interpret and perform. The profiles obtained by PMM analysis were easier to interpret than those obtained by RFLP or RAPD analysis. Bands that differed in staining intensity or that were of low intensity were observed by RAPD analysis, making interpretation more difficult. The reproducibilities with repeated runs of the same DNA preparation or with different DNA preparations of the same strain were high for all the methods. A high degree of genetic variation was observed in the test population, but isolates were not always similarly divided by each method. Interpretation of band profiles requires understanding of the molecular mechanisms responsible for genetic alternations. PMM analysis and Afut1 RFLP analysis, or their combination, appear to provide the best overall discriminatory power, reproducibility, ease of interpretation, and ease of use. This investigation will aid in planning epidemiologic and surveillance studies of A. fumigatus.

Aspergillosis↗
PubMed2003

The relationship of APOE genotype to neuropsychological performance in long-term cancer survivors treated with standard dose chemotherapy.

PURPOSE: The primary purpose of this study was to compare the neuropsychological performance of long-term survivors of breast cancer and lymphoma treated with standard dose chemotherapy who carried the epsilon 4 allele of the Apolipoprotein E (APOE) gene to those who carry other APOE alleles. PATIENTS AND METHODS: Long-term survivors (mean=8.8+/-4.3 years post-treatment) of breast cancer (N=51, age=55.9+/-8.8) or lymphoma (N=29, age=55.8+/-11.6) who had been treated with standard-dose chemotherapy completed a standardized battery of neuropsychological and psychological tests. Survivors were also classified into two groups based on the presence (N=17) or absence (N=63) of at least one epsilon 4 allele of APOE. RESULTS: Analysis of covariance, controlling for age, gender, education, diagnosis, and WRAT-3 reading subtest (a proxy measure of baseline IQ), indicated that survivors with at least one epsilon 4 allele scored significantly lower in the visual memory (p<0.03) and the spatial ability (p<0.05) domains and tended to score lower in the psychomotor functioning (p<0.08) domain as compared to survivors who did not carry an epsilon 4 allele. No group differences were found on depression, anxiety, or fatigue. CONCLUSIONS: The results of this study provide preliminary support for the hypothesis that the epsilon 4 allele of APOE may be a potential genetic marker for increased vulnerability to chemotherapy-induced cognitive decline.

Adult↗
PubMed1997

Use of a single-strand conformation polymorphism analysis to perform a simple genotyping of bovine kappa-casein A and B variants.

We propose an alternative method for casein genotyping, generally carried out using polymerase chain reaction followed by restriction fragment length polymorphism analysis. Application of the single-strand conformation polymorphism technique detects nucleotide changes in the fragment amplified by means of polymerase chain reaction and thus avoids the use of restriction enzymes. A 453 bp fragment from exon IV of kappa-casein has been amplified. The two variants (A and B), found with the highest frequencies in most bovine breeds and included in some dairy cattle selection schemes, can be discriminated using single-strand conformation polymorphism analysis of heat denatured fragments in acrylamide-bis-acrylamide (100:1) gels followed by silver staining. kappa-Casein genotyping is therefore simplified, although variants A and E on the one hand, and B and C on the other, are not distinguishable with this technique.

Animals↗
PubMed1991

Female genotype influences the behavioral performance of mice selected for reproductive traits.

The behavioral performance of mice that differ in regularity of the estrous cycle and litter size was studied after female exposure to a male of the same or a different strain. Emotional reactivity was measured using the pole, straightaway and open field tests. Factor interpretations of emotionality included motor discharge, autonomic imbalance and acrophobia. Mice characterized by regular estrous cycles and large litters (line E) were more explorative and emotionally reactive with respect to motor discharge and autonomic imbalance. In contrast, mice with less regular estrous cycles and small litter size (line CN-) were more acrophobic. These strain differences in behavioral performance were influenced by the genotype of the female rather than the cohabitating male.

Animals↗
PubMed2006

222 base pairs in NS5B region and the determination of hepatitis C virus genotype 6.

OBJECTIVE: The present study was performed to genotype hepatitis C virus (HCV) by direct sequencing of a 222-bp nucleotide in the NS5B region and comparing the results with those of direct sequencing in the core region. We investigated a new region for HCV genotyping which gave the best performance to discriminate HCV genotype 6a, the unique genotype found in Southeast Asia. METHODS: Plasma samples taken from 57 HCV-infected blood donors were used in this study. RT-PCR products were amplified using primers located in the NS5B region. The 222-bp PCR products were purified and sequenced. The genotype of HCV isolates were obtained by phylogenetic analysis and compared with HCV reference strains stored in the GenBank database. The HCV sequences clustering in the same node were considered to be of the same genotype. RESULTS: Thirty-one, 22 and 4 samples of HCV genotype 3a, 1a and 1b, respectively, were analyzed by this method. Upon comparison with genotyping in the core region, 86 and 14% of the samples yielded concordant and discordant genotype results, respectively. The majority of discordant results (63%; 5 of 8) was observed with HCV genotype 6a which yielded 6a upon core sequencing as opposed to 1a or 3a upon NS5B sequencing. CONCLUSION: HCV genotype 6a obtained by direct sequencing in the core region could not be unequivocally arrived at by sequencing 222 bp in the NS5B region. Hence, sequencing in the core region is preferable for genotyping our specimens, even though longer PCR products are required as this method enables discrimination between genotype 6a and the remaining genotypes.

Base Pairing↗